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BioC 3.4: CHECK report for KEGGgraph on morelia

This page was generated on 2016-09-21 03:50:14 -0700 (Wed, 21 Sep 2016).

Package 642/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGgraph 1.31.0
Jitao David Zhang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGgraph
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: KEGGgraph
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.31.0.tar.gz
StartedAt: 2016-09-20 08:25:31 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:26:23 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 52.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: KEGGgraph.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGgraph_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGgraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGgraph’ version ‘1.31.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘KEGGgraph’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘KEGG.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.subtypeDisplay: no visible global function definition for ‘data’
.subtypeDisplay: no visible binding for global variable
  ‘KEGGEdgeSubtype’
KEGGgraphLegend: no visible global function definition for ‘par’
KEGGgraphLegend: no visible global function definition for ‘data’
KEGGgraphLegend: no visible binding for global variable
  ‘KEGGEdgeSubtype’
KEGGgraphLegend: no visible global function definition for ‘text’
KEGGgraphLegend: no visible global function definition for ‘segments’
getCategoryIndepKGMLurl: no visible global function definition for
  ‘download.file’
kgmlFileName2PathwayName: no visible binding for global variable
  ‘KEGGPATHID2NAME’
parseKGMLexpandMaps: no visible global function definition for
  ‘download.file’
plotKEGGgraph: no visible global function definition for ‘layoutGraph’
plotKEGGgraph: no visible global function definition for ‘renderGraph’
retrieveKGML: no visible global function definition for ‘download.file’
subtypeDisplay,graph: no visible binding for global variable ‘test’
subtypeDisplay,graph: no visible binding for global variable
  ‘keggeEdgesDisplay’
Undefined global functions or variables:
  KEGGEdgeSubtype KEGGPATHID2NAME data download.file keggeEdgesDisplay
  layoutGraph par renderGraph segments test text
Consider adding
  importFrom("graphics", "par", "segments", "text")
  importFrom("utils", "data", "download.file")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘kegg2graph.R’
  Running ‘testGraph.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/KEGGgraph.Rcheck/00check.log’
for details.


KEGGgraph.Rcheck/00install.out:

* installing *source* package ‘KEGGgraph’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (KEGGgraph)

KEGGgraph.Rcheck/KEGGgraph-Ex.timings:

nameusersystemelapsed
KEGGEdge-class0.4100.0060.417
KEGGEdgeSubType-class0.0010.0000.001
KEGGEdgeSubtype0.0170.0030.020
KEGGGraphics-class0.0010.0000.001
KEGGGroup-class0.0000.0000.001
KEGGNode-class0.2420.0010.243
KEGGPathway-class0.3790.0060.385
KEGGPathwayInfo-class0.1880.0020.190
KEGGReaction-class0.3110.0010.312
KEGGpathway2Graph0.2070.0020.208
KEGGpathway2reactionGraph0.3320.0040.335
expandKEGGPathway0.3930.0010.395
getDisplayName-methods0.2550.0010.256
getEntryID-methods0.2190.0010.221
getKEGGID-methods0.1030.0010.103
getKEGGgeneLink-methods0.0010.0000.000
getKEGGnodeData0.5980.0020.602
getKGMLurl0.0040.0020.006
getName-methods0.2150.0020.218
getNamedElement000
getPathwayInfo-methods0.2650.0010.266
getReactions-methods0.3550.0010.355
getRgraphvizEdgeNames0.0020.0000.002
getSubtype-methods0.2360.0020.239
getTitle-methods0.2170.0000.217
getType-methods0.3750.0010.377
graphDensity0.0020.0000.002
isHomoList0.0000.0000.001
mergeKEGGgraphs1.1910.0061.199
neighborhood0.1610.0050.193
parseKGML0.2280.0010.229
parseKGML2DataFrame1.4380.0081.448
parseKGML2Graph0.5690.0030.572
plotKEGGgraph1.2170.0121.230
pvalue2asterisk0.0010.0000.001
queryKEGGsubgraph0.6840.0030.687
randomSubGraph0.0190.0000.019
splitKEGGgroup0.2090.0010.210
subGraphByNodeType0.5960.0030.600
subKEGGgraph0.6090.0020.613
translateKEGGID2GeneID0.0010.0000.001
translateKEGGgraph0.5760.0050.581